I am not sure of the exact nature of this question. It is relatively easy to transfer an AVR Studio program to an STK500 programmer, so I am guessing that this is not the problem.

Does the problem relate to the ability to send an old AVR Studio hex file to a target device via a Flowcode for AVR installation - possibly using an alternative programmer (AVRISPmkII)?

I have attached a batch file that automates the process of sending any hex file to a target device using the copy of AVRDUDE supplied with Flowcode for AVR. This provides support for the STK500, AVRISPmkII and many other programmers.

The batch file should be copied into the same folder as the hex file, and edited to provide the correct details: hex file name target device programmer programming port path to AVRDUDE I have also attached a copy of the AVRDUDE manual which includes lists of the programmers and target devices supported.